Package ‘Nozzle.R1’February 19, 2015
Type Package
Title Nozzle Reports
Version 1.1-1
Date 2012-05-15
Author Nils Gehlenborg <[email protected]>
Maintainer Nils Gehlenborg <[email protected]>
Description The Nozzle package provides an API to generate HTMLreports with dynamic user interface elements based onJavaScript and CSS (Cascading Style Sheets). Nozzle wasdesigned to facilitate summarization and rapid browsing ofcomplex results in data analysis pipelines where multipleanalyses are performed frequently on big data sets. The packagecan be applied to any project where user-friendly reports needto be created.
License LGPL-2
URL http://github.com/parklab/nozzle,
http://gdac.broadinstitute.org/nozzle
BugReports http://www.github.com/parklab/nozzle/issues
Copyright Nozzle is copyright 2013 The Fellows and President ofHarvard College and The Broad Institute, Inc. All rightsreserved. jQuery is licensed under the MIT license. Copyright2012 jQuery Foundation. jQuery Tablesorter plugin is licensedunder the MIT license. Copyright 2008 Christian Bach.
LazyLoad yes
Collate 'nozzle.R'
NeedsCompilation no
Repository CRAN
Date/Publication 2013-05-15 19:25:56
1
2 R topics documented:
R topics documented:Nozzle.R1-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4addTo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5addToInput . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6addToIntroduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6addToMeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7addToMethods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7addToOverview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8addToReferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9addToResults . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9addToSummary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10asCode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10asEmph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11asFilename . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11asLink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12asParameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12asReference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13asStrong . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13asSummary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14asValue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14DEFAULT.DOI.RESOLVER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15DEFAULT.REPORT.FILENAME . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15DEFAULT.SIGNIFICANT.ENTITY . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16getContactInformationEmail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16getContactInformationLabel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17getContactInformationMessage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17getContactInformationSubject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18getCopyrightOwner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18getCopyrightStatement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19getCopyrightUrl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19getCopyrightYear . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20getCreatorDate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20getCreatorName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21getCustomPrintCss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21getCustomScreenCss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22getDoi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22getDoiCreator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23getDoiPublisher . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23getDoiResolver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24getDoiTitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24getDoiVersion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25getDoiYear . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25getExportedElement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26getExportedElementIds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26getFigureFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27getFigureFileHighRes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28getGoogleAnalyticsId . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
R topics documented: 3
getLogo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29getMaintainerAffiliation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29getMaintainerEmail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30getMaintainerName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30getRendererDate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31getRendererName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31getReportId . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32getReportSubTitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32getReportTitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33getSignificantEntity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33getSignificantResultsCount . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34getSoftwareName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34getSoftwareVersion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35getSummary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35getTableFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36HTML.FRAGMENT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36HTML.REPORT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37IMAGE.TYPE.PDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37IMAGE.TYPE.RASTER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37IMAGE.TYPE.SVG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38isFigure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38isTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39LOGO.BOTTOM.CENTER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39LOGO.BOTTOM.LEFT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40LOGO.BOTTOM.RIGHT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40LOGO.TOP.CENTER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40LOGO.TOP.LEFT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41LOGO.TOP.RIGHT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41newCitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41newCustomReport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42newFigure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43newHtml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43newJournalCitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44newList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45newParagraph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45newParameterList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46newReport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47newResult . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47newSection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48newSubSection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49newSubSubSection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49newTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50newWebCitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51PROTECTION.GROUP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51PROTECTION.PRIVATE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52PROTECTION.PUBLIC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52PROTECTION.TCGA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52RDATA.REPORT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
4 Nozzle.R1-package
SECTION.CLASS.META . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53SECTION.CLASS.RESULTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53setContactInformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54setCopyright . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54setCustomPrintCss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55setCustomScreenCss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56setDoi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56setDoiCreator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57setDoiPublisher . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58setDoiResolver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58setDoiTitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59setDoiVersion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60setDoiYear . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60setFigureFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61setFigureFileHighRes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62setGoogleAnalyticsId . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62setLogo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63setMaintainerAffiliation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64setMaintainerEmail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64setMaintainerName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65setNextReport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65setParentReport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66setPreviousReport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67setReportSubTitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67setReportTitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68setSignificantEntity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68setSoftwareName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69setSoftwareVersion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70setTableFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70TABLE.SIGNIFICANT.DIGITS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71writeReport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Index 73
Nozzle.R1-package Nozzle: a Report Generation Toolkit for Data Analysis Pipelines
Description
Provides a high-level API to generate HTML reports with dynamic user interface elements.
Details
Package: Nozzle.R1Type: PackageVersion: 1.1-0Date: 2013-04-16
addTo 5
License: LGPL (>= 2)LazyLoad: yes
Nozzle was designed to facilitate summarization and rapid browsing of complex results in dataanalysis pipelines where multiple analyses are performed frequently on big data sets.
Note
The "R1" in the "Nozzle.R1" package name stands for "revision 1" of the Nozzle R API. All versionsof the Nozzle.R1 package will be backwards-compatible and able to render reports generated withearlier versions of the package. When backwards-compatibility of the API can no longer maintainedthe package name will change to "Nozzle.R2".
Author(s)
Nils Gehlenborg <[email protected]>
References
http://www.github.com/parklab/Nozzle, http://gdac.broadinstitute.org/nozzle
addTo Add child elements to a parent element.
Description
Add child elements to a parent element.
Usage
addTo(parent, ..., row = NA, column = NA)
Arguments
parent Parent element.... One or more child elements.row If parent element is a table row and column indices must be provided to add
supplementary results to cell in the table.column If parent element is a table row and column indices must be provided to add
supplementary results to cell in the table.
Value
Updated parent element.
Author(s)
Nils Gehlenborg <[email protected]>
6 addToIntroduction
addToInput Add elements to the "Input" subsection in the "Methods & Data" sec-tion of a standard report.
Description
Add elements to the "Input" subsection in the "Methods & Data" section of a standard report.
Usage
addToInput(report, ...)
Arguments
report Report element.
... Elements that will be added to the input section. Often these are paragraphelements.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
addToIntroduction Add elements to the "Introduction" subsection in the "Overview" sec-tion of a standard report.
Description
Add elements to the "Introduction" subsection in the "Overview" section of a standard report.
Usage
addToIntroduction(report, ...)
Arguments
report Report element.
... Elements that will be added to the introduction section. Often these are para-graph elements.
addToMeta 7
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
addToMeta Add elements to the "Meta" section of a standard report.
Description
Add elements to the "Meta" section of a standard report.
Usage
addToMeta(report, ...)
Arguments
report Report element.
... Elements that will be added to the references section. These may be any ele-ments.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
addToMethods Add elements to the "Methds & Data" section of a standard report.
Description
Add elements to the "Methds & Data" section of a standard report.
Usage
addToMethods(report, ...)
8 addToOverview
Arguments
report Report element.
... Elements that will be added to the methods section. Often these are subsectionelements.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
addToOverview Add elements to the "Overview" section of a standard report.
Description
Add elements to the "Overview" section of a standard report.
Usage
addToOverview(report, ...)
Arguments
report Report element.
... Elements that will be added to the overview section. Often these are subsectionelements.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
addToReferences 9
addToReferences Add elements to the "References" subsection in the "Methods & Data"section of a standard report.
Description
Add elements to the "References" subsection in the "Methods & Data" section of a standard report.
Usage
addToReferences(report, ...)
Arguments
report Report element.
... Elements that will be added to the references section. These should be citationelements.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
addToResults Add elements to the "Results" section of a standard report.
Description
Add elements to the "Results" section of a standard report.
Usage
addToResults(report, ...)
Arguments
report Report element.
... Elements that will be added to the results section. Often these are subsectionelements.
Value
Updated report element.
10 asCode
Author(s)
Nils Gehlenborg <[email protected]>
addToSummary Add elements to the "Summary" subsection in the "Overview" sectionof a standard report.
Description
Add elements to the "Summary" subsection in the "Overview" section of a standard report.
Usage
addToSummary(report, ...)
Arguments
report Report element.
... Elements that will be added to the overview section. Often these are paragraphelements.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
asCode Format text as code.
Description
Format text as code.
Usage
asCode(...)
Arguments
... One or more strings that will be concatenated.
asEmph 11
Value
Text formatted as a code.
Author(s)
Nils Gehlenborg <[email protected]>
asEmph Format text with emphasis (usually resulting in text set in italics).
Description
Format text with emphasis (usually resulting in text set in italics).
Usage
asEmph(...)
Arguments
... One or more strings that will be concatenated.
Value
Text with emphasis.
Author(s)
Nils Gehlenborg <[email protected]>
asFilename Format text as filename.
Description
Format text as filename.
Usage
asFilename(...)
Arguments
... One or more strings that will be concatenated.
12 asParameter
Value
Text formatted as a filename.
Author(s)
Nils Gehlenborg <[email protected]>
asLink Format text as a hyperlink.
Description
Format text as a hyperlink.
Usage
asLink(url, ...)
Arguments
url URL to be for the link.
... One or more strings that will be concatenated to form the text of the link.
Value
A hyperlink.
Author(s)
Nils Gehlenborg <[email protected]>
asParameter Format text as parameter.
Description
Format text as parameter.
Usage
asParameter(...)
Arguments
... One or more strings that will be concatenated.
asReference 13
Value
Text formatted as a parameter.
Author(s)
Nils Gehlenborg <[email protected]>
asReference Reference a citation, figure or table element.
Description
Reference a citation, figure or table element.
Usage
asReference(element)
Arguments
element Citation, figure or table element.
Value
A reference string for the referenced element that will be resolved when the report is written to fileand rendered to HTML.
Author(s)
Nils Gehlenborg <[email protected]>
asStrong Format text with strong emphasis (usually resulting in text set in bold).
Description
Format text with strong emphasis (usually resulting in text set in bold).
Usage
asStrong(...)
Arguments
... One or more strings that will be concatenated.
14 asValue
Value
Text with strong emphasis.
Author(s)
Nils Gehlenborg <[email protected]>
asSummary Include a result in text. This is a legacy method and provided only forbackwards compatibility.
Description
Include a result in text. This is a legacy method and provided only for backwards compatibility.
Usage
asSummary(result)
Arguments
result The result element.
Value
The result element.
Author(s)
Nils Gehlenborg <[email protected]>
asValue Format text as value.
Description
Format text as value.
Usage
asValue(...)
Arguments
... One or more strings that will be concatenated.
DEFAULT.DOI.RESOLVER 15
Value
Text formatted as a value.
Author(s)
Nils Gehlenborg <[email protected]>
DEFAULT.DOI.RESOLVER Default DOI resolver URL.
Description
Default DOI resolver URL.
Usage
DEFAULT.DOI.RESOLVER
Format
chr "http://dx.doi.org"
DEFAULT.REPORT.FILENAME
Default filename for reports.
Description
Default filename for reports.
Usage
DEFAULT.REPORT.FILENAME
Format
chr "nozzle"
16 getContactInformationEmail
DEFAULT.SIGNIFICANT.ENTITY
Name of entities that are labeled as signficiant.
Description
Name of entities that are labeled as signficiant.
Usage
DEFAULT.SIGNIFICANT.ENTITY
Format
chr "statistically significant findings"
getContactInformationEmail
Get contact email address for report.
Description
Get contact email address for report.
Usage
getContactInformationEmail(report)
Arguments
report Report element.
Value
Contact email address.
Author(s)
Nils Gehlenborg <[email protected]>
getContactInformationLabel 17
getContactInformationLabel
Get label for contact button for report.
Description
Get label for contact button for report.
Usage
getContactInformationLabel(report)
Arguments
report Report element.
Value
Contact email button label.
Author(s)
Nils Gehlenborg <[email protected]>
getContactInformationMessage
Get contact email default message for report.
Description
Get contact email default message for report.
Usage
getContactInformationMessage(report)
Arguments
report Report element.
Value
Contact email default message.
Author(s)
Nils Gehlenborg <[email protected]>
18 getCopyrightOwner
getContactInformationSubject
Get contact email subject line for report.
Description
Get contact email subject line for report.
Usage
getContactInformationSubject(report)
Arguments
report Report element.
Value
Contact email subject line.
Author(s)
Nils Gehlenborg <[email protected]>
getCopyrightOwner Get name of the copyright owner for report.
Description
Get name of the copyright owner for report.
Usage
getCopyrightOwner(report)
Arguments
report Report element.
Value
Name of the copyright owner.
Author(s)
Nils Gehlenborg <[email protected]>
getCopyrightStatement 19
getCopyrightStatement Get copyright statement for report. This text is linked to the copyrightURL.
Description
Get copyright statement for report. This text is linked to the copyright URL.
Usage
getCopyrightStatement(report)
Arguments
report Report element.
Value
Text of the c opyright statement.
Author(s)
Nils Gehlenborg <[email protected]>
getCopyrightUrl Get copyright URL for report, which is linked to the copyright state-ment.
Description
Get copyright URL for report, which is linked to the copyright statement.
Usage
getCopyrightUrl(report)
Arguments
report Report element.
Value
Copyright URL.
Author(s)
Nils Gehlenborg <[email protected]>
20 getCreatorDate
getCopyrightYear Get copyright year report.
Description
Get copyright year report.
Usage
getCopyrightYear(report)
Arguments
report Report element.
Value
Copyright year.
Author(s)
Nils Gehlenborg <[email protected]>
getCreatorDate Get date when report was created.
Description
Get date when report was created.
Usage
getCreatorDate(report)
Arguments
report Report element.
Value
Date when report was created or NA.
Author(s)
Nils Gehlenborg <[email protected]>
getCreatorName 21
getCreatorName Get name and version of the Nozzle package that was used to createreport.
Description
Get name and version of the Nozzle package that was used to create report.
Usage
getCreatorName(report)
Arguments
report Report element.
Value
Name and version of the Nozzle package that created report or NA.
Author(s)
Nils Gehlenborg <[email protected]>
getCustomPrintCss Get the path or URL of the CSS file to be used to overwrite the defaultprint (not: screen) style sheet.
Description
Get the path or URL of the CSS file to be used to overwrite the default print (not: screen) stylesheet.
Usage
getCustomPrintCss(report)
Arguments
report Report element.
Value
Path or URL of CSS file. Can be relative or absolute.
Author(s)
Nils Gehlenborg <[email protected]>
22 getDoi
getCustomScreenCss Get the path or URL of the CSS file to be used to overwrite the defaultscreen (not: print) style sheet.
Description
Get the path or URL of the CSS file to be used to overwrite the default screen (not: print) stylesheet.
Usage
getCustomScreenCss(report)
Arguments
report Report element.
Value
Path or URL of CSS file. Can be relative or absolute.
Author(s)
Nils Gehlenborg <[email protected]>
getDoi Get the DOI (document object identifier, http://www.doi.org) forreport.
Description
Get the DOI (document object identifier, http://www.doi.org) for report.
Usage
getDoi(report)
Arguments
report Report element.
Value
Document object identifier (DOI) for report.
Author(s)
Nils Gehlenborg <[email protected]>
getDoiCreator 23
getDoiCreator Get the DOI creator for report.
Description
Get the DOI creator for report.
Usage
getDoiCreator(report)
Arguments
report Report element.
Value
Creator associated with the DOI of the report report.
Author(s)
Nils Gehlenborg <[email protected]>
getDoiPublisher Get the DOI publisher for report.
Description
Get the DOI publisher for report.
Usage
getDoiPublisher(report)
Arguments
report Report element.
Value
Publisher associated with the DOI of the report report.
Author(s)
Nils Gehlenborg <[email protected]>
24 getDoiTitle
getDoiResolver Get the DOI resolver URL (e.g. http://dx.doi.org) for report.
Description
Get the DOI resolver URL (e.g. http://dx.doi.org) for report.
Usage
getDoiResolver(report)
Arguments
report Report element.
Value
Document object identifier (DOI) resolver URL for report.
Author(s)
Nils Gehlenborg <[email protected]>
getDoiTitle Get the DOI title for report.
Description
Get the DOI title for report.
Usage
getDoiTitle(report)
Arguments
report Report element.
Value
Title associated with the DOI of the report report.
Author(s)
Nils Gehlenborg <[email protected]>
getDoiVersion 25
getDoiVersion Get the DOI version for report.
Description
Get the DOI version for report.
Usage
getDoiVersion(report)
Arguments
report Report element.
Value
Version associated with the DOI of the report report.
Author(s)
Nils Gehlenborg <[email protected]>
getDoiYear Get the DOI year for report.
Description
Get the DOI year for report.
Usage
getDoiYear(report)
Arguments
report Report element.
Value
Publication year associated with the DOI of the report report.
Author(s)
Nils Gehlenborg <[email protected]>
26 getExportedElementIds
getExportedElement Get an exported element from a report. This can be used to generateaggregate reports. This is an experimental feature of Nozzle and maynot lead to the expected results.
Description
Get an exported element from a report. This can be used to generate aggregate reports. This is anexperimental feature of Nozzle and may not lead to the expected results.
Usage
getExportedElement(report, exportId)
Arguments
report The source report.
exportId The ID of the exported element. getExportedElementIds returns a list of ex-ported element IDs.
Value
The exported report element or NULL if the ID does not exist in report.
Note
Elements containing references should not be exported since references cannot be resolved in thetarget report. Relative paths in exported elements may have to be adjusted manually if the targetreport will be located in a different directory.
Author(s)
Nils Gehlenborg <[email protected]>
getExportedElementIds Get the IDs of exported elements from report. This is an experimentalfeature of Nozzle and may not lead to the expected results.
Description
Get the IDs of exported elements from report. This is an experimental feature of Nozzle and maynot lead to the expected results.
Usage
getExportedElementIds(report)
getFigureFile 27
Arguments
report The source report.
Value
The IDs of exported report elements or NULL.
Author(s)
Nils Gehlenborg <[email protected]>
getFigureFile Get path or URL of image file associated with a figure element.
Description
Get path or URL of image file associated with a figure element.
Usage
getFigureFile(element)
Arguments
element Figure element.
Value
Path or URL of the image file or NA if element is not a figure.
Author(s)
Nils Gehlenborg <[email protected]>
28 getGoogleAnalyticsId
getFigureFileHighRes Get path or URL of high-resolution of vector-based image file associ-ated with a figure element.
Description
Get path or URL of high-resolution of vector-based image file associated with a figure element.
Usage
getFigureFileHighRes(element)
Arguments
element Figure element.
Value
Path or URL of the image file or NA if element is not a figure.
Author(s)
Nils Gehlenborg <[email protected]>
getGoogleAnalyticsId Get Google Analytics tracking ID for report.
Description
Get Google Analytics tracking ID for report.
Usage
getGoogleAnalyticsId(report)
Arguments
report Report element.
Value
Google Analytics Tracking ID or NA if not set.
Author(s)
Nils Gehlenborg <[email protected]>
getLogo 29
getLogo Get logo file for one of six positions (three at the top, three at thebottom) in report.
Description
Get logo file for one of six positions (three at the top, three at the bottom) in report.
Usage
getLogo(report, position)
Arguments
report Report element.
position One of LOGO.TOP.LEFT, LOGO.TOP.CENTER, LOGO.TOP.RIGHT, LOGO.BOTTOM.LEFT,LOGO.BOTTOM.CENTER, LOGO.BOTTOM.RIGHT.
Value
Path or URL to the logo file at position.
Author(s)
Nils Gehlenborg <[email protected]>
getMaintainerAffiliation
Get affiliation of maintainer of report.
Description
Get affiliation of maintainer of report.
Usage
getMaintainerAffiliation(report)
Arguments
report Report element.
Value
Affiliation of the maintainer.
30 getMaintainerName
Author(s)
Nils Gehlenborg <[email protected]>
getMaintainerEmail Get email address of maintainer of report.
Description
Get email address of maintainer of report.
Usage
getMaintainerEmail(report)
Arguments
report Report element.
Value
Email address of the maintainer.
Author(s)
Nils Gehlenborg <[email protected]>
getMaintainerName Get name of maintainer of report.
Description
Get name of maintainer of report.
Usage
getMaintainerName(report)
Arguments
report Report element.
Value
Name of the maintainer.
Author(s)
Nils Gehlenborg <[email protected]>
getRendererDate 31
getRendererDate Get date when report was rendered.
Description
Get date when report was rendered.
Usage
getRendererDate(report)
Arguments
report Report element.
Value
Date when report was rendered or NA.
Author(s)
Nils Gehlenborg <[email protected]>
getRendererName Get name and version of the Nozzle package that was used to renderreport.
Description
Get name and version of the Nozzle package that was used to render report.
Usage
getRendererName(report)
Arguments
report Report element.
Value
Name and version of the Nozzle package that rendered report or NA.
Author(s)
Nils Gehlenborg <[email protected]>
32 getReportSubTitle
getReportId Get the ID (a UUID) of report.
Description
Get the ID (a UUID) of report.
Usage
getReportId(report)
Arguments
report Report element.
Value
ID of report or NA.
Author(s)
Nils Gehlenborg <[email protected]>
getReportSubTitle Get the subtitle of report.
Description
Get the subtitle of report.
Usage
getReportSubTitle(report)
Arguments
report Report element.
Value
SubTitle of report
Author(s)
Nils Gehlenborg <[email protected]>
getReportTitle 33
getReportTitle Get the title of report.
Description
Get the title of report.
Usage
getReportTitle(report)
Arguments
report Report element.
Value
Title of report
Author(s)
Nils Gehlenborg <[email protected]>
getSignificantEntity Get name of entities that are called out as significant, e.g. "gene".This is currently not being used and might become obsolete in futureversions of Nozzle.
Description
Get name of entities that are called out as significant, e.g. "gene". This is currently not being usedand might become obsolete in future versions of Nozzle.
Usage
getSignificantEntity(report)
Arguments
report Report element.
Value
Name of entities called out as significant.
Author(s)
Nils Gehlenborg <[email protected]>
34 getSoftwareName
getSignificantResultsCount
Get the total number of significant results in report.
Description
Get the total number of significant results in report.
Usage
getSignificantResultsCount(report)
Arguments
report The report.
Value
Number of signficiant results.
Author(s)
Nils Gehlenborg <[email protected]>
getSoftwareName Get the name of the software that used Nozzle to generate report.
Description
Get the name of the software that used Nozzle to generate report.
Usage
getSoftwareName(report)
Arguments
report Report element.
Value
Name of the software that used Nozzle to generate report.
Author(s)
Nils Gehlenborg <[email protected]>
getSoftwareVersion 35
getSoftwareVersion Get the version of the software that used Nozzle to generate report.
Description
Get the version of the software that used Nozzle to generate report.
Usage
getSoftwareVersion(report)
Arguments
report Report element.
Value
Version of the software that used Nozzle to generate report.
Author(s)
Nils Gehlenborg <[email protected]>
getSummary Get the first element of the "Summary" subsection in the "Overview"section in a standard report.
Description
Get the first element of the "Summary" subsection in the "Overview" section in a standard report.
Usage
getSummary(report)
Arguments
report The report.
Value
A report element.
Author(s)
Nils Gehlenborg <[email protected]>
36 HTML.FRAGMENT
getTableFile Get path or URL of file associatd with table element.
Description
Get path or URL of file associatd with table element.
Usage
getTableFile(element)
Arguments
element Table element.
Value
Path or URL.
Author(s)
Nils Gehlenborg <[email protected]>
HTML.FRAGMENT Output type.
Description
Output type.
Usage
HTML.FRAGMENT
Format
chr "html_fragment"
HTML.REPORT 37
HTML.REPORT Output type.
Description
Output type.
Usage
HTML.REPORT
Format
chr "html_standalone"
IMAGE.TYPE.PDF Image type.
Description
Image type.
Usage
IMAGE.TYPE.PDF
Format
num 2
IMAGE.TYPE.RASTER Image type.
Description
Image type.
Usage
IMAGE.TYPE.RASTER
Format
num 0
38 isFigure
IMAGE.TYPE.SVG Image type.
Description
Image type.
Usage
IMAGE.TYPE.SVG
Format
num 1
isFigure Test if element is a figure element.
Description
Test if element is a figure element.
Usage
isFigure(element)
Arguments
element Element to test.
Value
TRUE if the element is a figure, FALSE otherwise.
Author(s)
Nils Gehlenborg <[email protected]>
isTable 39
isTable Test if element is a table element.
Description
Test if element is a table element.
Usage
isTable(element)
Arguments
element Element to test.
Value
TRUE if the element is a table, FALSE otherwise.
Author(s)
Nils Gehlenborg <[email protected]>
LOGO.BOTTOM.CENTER Logo position.
Description
Logo position.
Usage
LOGO.BOTTOM.CENTER
Format
num 16
40 LOGO.TOP.CENTER
LOGO.BOTTOM.LEFT Logo position.
Description
Logo position.
Usage
LOGO.BOTTOM.LEFT
Format
num 8
LOGO.BOTTOM.RIGHT Logo position.
Description
Logo position.
Usage
LOGO.BOTTOM.RIGHT
Format
num 32
LOGO.TOP.CENTER Logo position.
Description
Logo position.
Usage
LOGO.TOP.CENTER
Format
num 2
LOGO.TOP.LEFT 41
LOGO.TOP.LEFT Logo position.
Description
Logo position.
Usage
LOGO.TOP.LEFT
Format
num 1
LOGO.TOP.RIGHT Logo position.
Description
Logo position.
Usage
LOGO.TOP.RIGHT
Format
num 4
newCitation Create a citation element.
Description
Create a citation element.
Usage
newCitation(authors = "", title, publication = "",issue = "", number = "", pages = "", year = "",url = "")
42 newCustomReport
Arguments
authors Names of authors.
title Title of the document.
publication Name of the publication where the document appeared.
issue Issue of the publication.
number Number of the publication.
pages Pages of the document in the publication.
year Year when the document was published.
url URL of the document.
Value
New element.
Author(s)
Nils Gehlenborg <[email protected]>
newCustomReport Create a new custom report without pre-defined sections.
Description
Create a new custom report without pre-defined sections.
Usage
newCustomReport(..., version = 0)
Arguments
... One or more strings that will be concatenated into the report title.
version Version number. Not in use.
Value
A new report element.
Author(s)
Nils Gehlenborg ([email protected])
newFigure 43
newFigure Create a new list element.
Description
Create a new list element.
Usage
newFigure(file, ..., fileHighRes = NA,type = IMAGE.TYPE.RASTER, exportId = NULL,protection = PROTECTION.PUBLIC)
Arguments
file Path or URL to the image file. Paths can be absolute or relative.
... Strings that will be concatenated to form the figure caption.
fileHighRes Path or URL to a high-resolution or vector-based version of the image file. Pathscan be absolute or relative.
type Currenlty only IMAGE.TYPE.RASTER is allowed.
exportId Unique string to identify this element. Used to retrieve the element using getExportedElement.
protection Procection level. One of PROTECTION.PUBLIC, PROTECTION.GROUP, PRO-TECTION.PRIVATE.
Value
New element.
Author(s)
Nils Gehlenborg <[email protected]>
newHtml Create a new freeform HTML element. THIS MUST BE USED WITHEXTRAORDINARTY CARE!
Description
Create a new freeform HTML element. THIS MUST BE USED WITH EXTRAORDINARTYCARE!
Usage
newHtml(..., style = NULL, exportId = NULL,protection = PROTECTION.PUBLIC)
44 newJournalCitation
Arguments
... Strings that will be concatenated to form the HTML content that will be wrappedinto a div element.
style CSS to be applied to the div element.
exportId Unique string to identify this element. Used to retrieve the element using getExportedElement.
protection Procection level. One of PROTECTION.PUBLIC, PROTECTION.GROUP, PRO-TECTION.PRIVATE.
Value
New element.
Author(s)
Nils Gehlenborg <[email protected]>
newJournalCitation Create a citation element that represents a document published in ajournal. This is a convenience wrapper for newCitation.
Description
Create a citation element that represents a document published in a journal. This is a conveniencewrapper for newCitation.
Usage
newJournalCitation(authors, title, publication, issue,number, pages, year, url = "")
Arguments
authors Names of authors.
title Title of the document.
publication Name of the publication where the document appeared.
issue Issue of the publication.
number Number of the publication.
pages Pages of the document in the publication.
year Year when the document was published.
url URL of the document.
Value
New element.
newList 45
Author(s)
Nils Gehlenborg <[email protected]>
newList Create a new list element.
Description
Create a new list element.
Usage
newList(..., isNumbered = FALSE, exportId = NULL,protection = PROTECTION.PUBLIC)
Arguments
... Elements of type paragraph, list or result that will form the items in the list.
isNumbered If set to FALSE, the list will be unordered with bullet points. If set to TRUE, thelist will be numbered with arabic numerals.
exportId Unique string to identify this element. Used to retrieve the element using getExportedElement.
protection Procection level. One of PROTECTION.PUBLIC, PROTECTION.GROUP orPROTECTION.PRIVATE.
Value
New element.
Author(s)
Nils Gehlenborg <[email protected]>
newParagraph Create a new paragraph element.
Description
Create a new paragraph element.
Usage
newParagraph(..., exportId = NULL,protection = PROTECTION.PUBLIC)
46 newParameterList
Arguments
... Strings that will be concatenated to form the text of the paragraph.
exportId Unique string to identify this element. Used to retrieve the element using getExportedElement.
protection Procection level. One of PROTECTION.PUBLIC, PROTECTION.GROUP, PRO-TECTION.PRIVATE.
Value
New element.
Author(s)
Nils Gehlenborg <[email protected]>
newParameterList Create a new parameter list element. A parameter list is an unnum-bered list of the form param_1 = value_1, ..., param_n = value_nwhere param_i is formated as a parameter and value_i is formatted asa value.
Description
Create a new parameter list element. A parameter list is an unnumbered list of the form param_1 =value_1, ..., param_n = value_n where param_i is formated as a parameter and value_i is formattedas a value.
Usage
newParameterList(..., separator = " = ", exportId = NULL,protection = PROTECTION.PUBLIC)
Arguments
... 2n strings that will be concatenated to form the parameter-value pairs. Stringsat positions 1, ..., 2n - 1 will be treated as parameters 1 through n and strings atpositions 2, ..., 2n will be treated as values 1 through n.
separator String to be used to separate parameters and values. Whitespace characters needto be supplied if required.
exportId Unique string to identify this element. Used to retrieve the element using getExportedElement.
protection Procection level. One of PROTECTION.PUBLIC, PROTECTION.GROUP, PRO-TECTION.PRIVATE.
Value
New element.
newReport 47
Author(s)
Nils Gehlenborg <[email protected]>
newReport Create a new report with pre-defined sections Overview/Introduction,Overview/Summary, Results, Methods & Data/Input, Methods &Data/References and Meta Data.
Description
Create a new report with pre-defined sections Overview/Introduction, Overview/Summary, Results,Methods & Data/Input, Methods & Data/References and Meta Data.
Usage
newReport(..., version = 0)
Arguments
... One or more strings that will be concatenated into the report title.
version Version number. Not in use.
Value
A new report element.
Author(s)
Nils Gehlenborg ([email protected])
newResult Create a new result element.
Description
Create a new result element.
Usage
newResult(..., isSignificant = FALSE,protection = PROTECTION.PUBLIC)
48 newSection
Arguments
... One or more strings that will be concatenated to form the text associated withthe result (often just a scalar or single string).
isSignificant If TRUE, the result will be declared signficant.
protection Procection level. One of PROTECTION.PUBLIC, PROTECTION.GROUP, PRO-TECTION.PRIVATE.
Value
New element.
Author(s)
Nils Gehlenborg <[email protected]>
newSection Create a new section element.
Description
Create a new section element.
Usage
newSection(..., class = "", exportId = NULL,protection = PROTECTION.PUBLIC)
Arguments
... Strings that will be concatenated to form the section title.
class If set to SECTION.CLASS.RESULTS, results can be reported in this section. Ifset to SECTION.CLASS.META the section will be a meta data section.
exportId Unique string to identify this element. Used to retrieve the element using getExportedElement.
protection Procection level. One of PROTECTION.PUBLIC, PROTECTION.GROUP, PRO-TECTION.PRIVATE.
Value
New element.
Author(s)
Nils Gehlenborg <[email protected]>
newSubSection 49
newSubSection Create a new subsection element.
Description
Create a new subsection element.
Usage
newSubSection(..., exportId = NULL,protection = PROTECTION.PUBLIC)
Arguments
... Strings that will be concatenated to form the subsection title.
exportId Unique string to identify this element. Used to retrieve the element using getExportedElement.
protection Procection level. One of PROTECTION.PUBLIC, PROTECTION.GROUP, PRO-TECTION.PRIVATE.
Value
New element.
Author(s)
Nils Gehlenborg <[email protected]>
newSubSubSection Create a new subsubsection element.
Description
Create a new subsubsection element.
Usage
newSubSubSection(..., exportId = NULL,protection = PROTECTION.PUBLIC)
Arguments
... Strings that will be concatenated to form the subsubsection title.
exportId Unique string to identify this element. Used to retrieve the element using getExportedElement.
protection Procection level. One of PROTECTION.PUBLIC, PROTECTION.GROUP, PRO-TECTION.PRIVATE.
50 newTable
Value
New element.
Author(s)
Nils Gehlenborg <[email protected]>
newTable Create new table element.
Description
Create new table element.
Usage
newTable(table, ..., file = NA,significantDigits = TABLE.SIGNIFICANT.DIGITS,exportId = NULL, protection = PROTECTION.PUBLIC)
Arguments
table A matrix or data frame containing the table data. Column names will be ex-tracted and used as column headers.
... Strings that will be concatenated to form the table caption.
file Path or URL to a file containing the full table. It is recommend to only show arelevant subset of all results in the report itself to increase readability.
significantDigits
Number of significant digits used to trim all numeric columns. The default isTABLE.SIGNIFICANT.DIGITS.
exportId Unique string to identify this element. Used to retrieve the element using getExportedElement.
protection Procection level. One of PROTECTION.PUBLIC, PROTECTION.GROUP, PRO-TECTION.PRIVATE.
Value
New element.
Author(s)
Nils Gehlenborg <[email protected]>
newWebCitation 51
newWebCitation Create a citation element that represents a document published online.This is a convenience wrapper for newCitation.
Description
Create a citation element that represents a document published online. This is a convenience wrap-per for newCitation.
Usage
newWebCitation(authors, title, url)
Arguments
authors Names of authors.
title Title of the document.
url URL of the document.
Value
New element.
Author(s)
Nils Gehlenborg <[email protected]>
PROTECTION.GROUP Group visibility.
Description
Group visibility.
Usage
PROTECTION.GROUP
Format
num 5
52 PROTECTION.TCGA
PROTECTION.PRIVATE Private visibility.
Description
Private visibility.
Usage
PROTECTION.PRIVATE
Format
num 10
PROTECTION.PUBLIC Public visibility.
Description
Public visibility.
Usage
PROTECTION.PUBLIC
Format
num 0
PROTECTION.TCGA Group visibility.
Description
Group visibility.
Usage
PROTECTION.TCGA
Format
num 5
RDATA.REPORT 53
RDATA.REPORT Output type.
Description
Output type.
Usage
RDATA.REPORT
Format
chr "rdata"
SECTION.CLASS.META Section class.
Description
Section class.
Usage
SECTION.CLASS.META
Format
chr "meta"
SECTION.CLASS.RESULTS Section class.
Description
Section class.
Usage
SECTION.CLASS.RESULTS
Format
chr "results"
54 setCopyright
setContactInformation Set contact information for report. This is used to create a "contact"button in the top right corner of the report, e.g. to collect feedbackabout the report.
Description
Set contact information for report. This is used to create a "contact" button in the top right cornerof the report, e.g. to collect feedback about the report.
Usage
setContactInformation(report, email, subject, message,label = NA)
Arguments
report Report element.
email Email address of the recipient of contact emails.
subject Subject of the email to be sent.
message Message used to pre-populate the email body.
label Label for the button, e.g. "Contact Us".
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
setCopyright Set copyright messsage for report.
Description
Set copyright messsage for report.
Usage
setCopyright(report, owner, year, statement = NA,url = NA)
setCustomPrintCss 55
Arguments
report Report element.
owner Copyright owner, e.g. "The President and Fellows of Harvard College".
year Copyright year, e.g. "2012" or "2011-2013".
statement Copyright statement, e.g. "All rights reserved.".
url A URL that will be linked to the copyright owner.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
setCustomPrintCss Set the path or URL of the CSS file to be used to overwrite the defaultprint (not: screen) style sheet. Can be relative or absolute.
Description
Set the path or URL of the CSS file to be used to overwrite the default print (not: screen) style sheet.Can be relative or absolute.
Usage
setCustomPrintCss(report, cssFile)
Arguments
report Report element.
cssFile URL or a relative or absolute path to a CSS file.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
56 setDoi
setCustomScreenCss Set the path or URL of the CSS file to be used to overwrite the defaultscreen (not: print) style sheet. Can be relative or absolute.
Description
Set the path or URL of the CSS file to be used to overwrite the default screen (not: print) style sheet.Can be relative or absolute.
Usage
setCustomScreenCss(report, cssFile)
Arguments
report Report element.
cssFile URL or a relative or absolute path to a CSS file.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
setDoi Set the DOI (document object identifier, http://www.doi.org) forreport. A warning will be emitted if the report has been assigneda DOI before.
Description
Set the DOI (document object identifier, http://www.doi.org) for report. A warning will be emittedif the report has been assigned a DOI before.
Usage
setDoi(report, doi)
Arguments
report Report element.
doi The document object identifier.
setDoiCreator 57
Value
Updated report element.
Note
A document object identifer must have been created before this is called.
Author(s)
Nils Gehlenborg <[email protected]>
References
http://www.doi.org
setDoiCreator Set the DOI meta data creator for report.
Description
Set the DOI meta data creator for report.
Usage
setDoiCreator(report, creator)
Arguments
report Report element.
creator Name of the report creator/author.
Value
Updated report element.
Note
This should match the meta data stored for the DOI.
Author(s)
Nils Gehlenborg <[email protected]>
58 setDoiResolver
setDoiPublisher Set the DOI meta data publisher for report.
Description
Set the DOI meta data publisher for report.
Usage
setDoiPublisher(report, publisher)
Arguments
report Report element.
publisher Publisher of the report.
Value
Updated report element.
Note
This should match the meta data stored for the DOI.
Author(s)
Nils Gehlenborg <[email protected]>
setDoiResolver Set the DOI resolver URL (e.g. http://dx.doi.org) for report. TheURL must not end with a slash!
Description
Set the DOI resolver URL (e.g. http://dx.doi.org) for report. The URL must not end with a slash!
Usage
setDoiResolver(report, url)
Arguments
report Report element.
url The resolver URL (without a trailing slash). The default is "http://dx.doi.org".
setDoiTitle 59
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
setDoiTitle Set the DOI meta data title for report.
Description
Set the DOI meta data title for report.
Usage
setDoiTitle(report, title)
Arguments
report Report element.
title Title of the report.
Value
Updated report element.
Note
This should match the meta data stored for the DOI.
Author(s)
Nils Gehlenborg <[email protected]>
60 setDoiYear
setDoiVersion Set the DOI meta data version for report.
Description
Set the DOI meta data version for report.
Usage
setDoiVersion(report, version)
Arguments
report Report element.
version Version of the report.
Value
Updated report element.
Note
This should match the meta data stored for the DOI.
Author(s)
Nils Gehlenborg <[email protected]>
setDoiYear Set the DOI meta data year for report.
Description
Set the DOI meta data year for report.
Usage
setDoiYear(report, year)
Arguments
report Report element.
year Publication year of the report.
setFigureFile 61
Value
Updated report element.
Note
This should match the meta data stored for the DOI.
Author(s)
Nils Gehlenborg <[email protected]>
setFigureFile Set path or URL of image file associated with a figure element. Pathscan relative or absolute.
Description
Set path or URL of image file associated with a figure element. Paths can relative or absolute.
Usage
setFigureFile(element, file)
Arguments
element A figure element.
file Path or URL of the image file.
Value
Updated figure element or NA is element is not a figure.
Author(s)
Nils Gehlenborg <[email protected]>
62 setGoogleAnalyticsId
setFigureFileHighRes Set path or URL of high-resolution or vector-based image file associ-ated with a figure element. Paths can be relative or absolute.
Description
Set path or URL of high-resolution or vector-based image file associated with a figure element.Paths can be relative or absolute.
Usage
setFigureFileHighRes(element, file)
Arguments
element A figure element.
file Path or URL of the image file.
Value
Updated figure element or NA is element is not a figure.
Author(s)
Nils Gehlenborg <[email protected]>
setGoogleAnalyticsId Set the Google Analytics tracking ID to be embedded in this report("web property id", usually starts with "UA-").
Description
Set the Google Analytics tracking ID to be embedded in this report ("web property id", usuallystarts with "UA-").
Usage
setGoogleAnalyticsId(report, id)
Arguments
report Report element.
id Web property ID for the Google Analytics tracking account.
setLogo 63
Value
Updated report element.
Note
A (free) Google Analytics account is required.
Author(s)
Nils Gehlenborg <[email protected]>
References
http://www.google.com/analytics
setLogo Set a logo file for one of six positions (three at the top, three at thebottom) in report, e.g. an institute logo.
Description
Set a logo file for one of six positions (three at the top, three at the bottom) in report, e.g. aninstitute logo.
Usage
setLogo(report, filename, position)
Arguments
report Report element.
filename Path or URL to the logo file (relative) to the final location of the report HTMLfile.
position One of LOGO.TOP.LEFT, LOGO.TOP.CENTER, LOGO.TOP.RIGHT, LOGO.BOTTOM.LEFT,LOGO.BOTTOM.CENTER, LOGO.BOTTOM.RIGHT.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
64 setMaintainerEmail
setMaintainerAffiliation
Set affiliation of maintainer of report.
Description
Set affiliation of maintainer of report.
Usage
setMaintainerAffiliation(report, ...)
Arguments
report Report element.
... One or more strings that will be concatenated to form the affiliation of the main-tainer.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
setMaintainerEmail Set email address of maintainer of report.
Description
Set email address of maintainer of report.
Usage
setMaintainerEmail(report, ...)
Arguments
report Report element.
... One or more strings that will be concatenated to form the email address of themaintainer.
Value
Updated report element.
setMaintainerName 65
Author(s)
Nils Gehlenborg <[email protected]>
setMaintainerName Set name of maintainer of report.
Description
Set name of maintainer of report.
Usage
setMaintainerName(report, ...)
Arguments
report Report element.
... One or more strings that will be concatenated to form the name of the maintainer.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
setNextReport Set the URL and title of the "next" report after report. This will beaccessible through the utility menu.
Description
Set the URL and title of the "next" report after report. This will be accessible through the utilitymenu.
Usage
setNextReport(report, url, ...)
Arguments
report Report object.
url URL of the next report.
... One or more strings that will be concatenated to form the title of the next report.
66 setParentReport
Value
Updated report element.
Author(s)
nils
setParentReport Set the URL and title of the "parent" report above report. This willbe accessible through the utility menu.
Description
Set the URL and title of the "parent" report above report. This will be accessible through theutility menu.
Usage
setParentReport(report, url, ...)
Arguments
report Report object.
url URL of the next report.
... One or more strings that will be concatenated to form the title of the parentreport.
Value
Updated report element.
Author(s)
nils
setPreviousReport 67
setPreviousReport Set the URL and title of the "previous" report before report. This willbe accessible through the utility menu.
Description
Set the URL and title of the "previous" report before report. This will be accessible through theutility menu.
Usage
setPreviousReport(report, url, ...)
Arguments
report Report object.
url URL of the next report.
... One or more strings that will be concatenated to form the title of the previousreport.
Value
Updated report element.
Author(s)
nils
setReportSubTitle Set the subtitle of report.
Description
Set the subtitle of report.
Usage
setReportSubTitle(report, ...)
Arguments
report Report element.
... One or more strings that will be concatenated to form the subtitle of the report.
68 setSignificantEntity
Value
Updated report element or NA if report has no subtitle element.
Author(s)
Nils Gehlenborg <[email protected]>
setReportTitle Set the title of report.
Description
Set the title of report.
Usage
setReportTitle(report, ...)
Arguments
report Report element.
... One or more strings that will be concatenated to form the title of the report.
Value
Updated report element or NA if report has no title element.
Author(s)
Nils Gehlenborg <[email protected]>
setSignificantEntity Set name of entities that are called out as significant, e.g. "gene".This is currently not being used and might become obsolete in futureversions of Nozzle.
Description
Set name of entities that are called out as significant, e.g. "gene". This is currently not being usedand might become obsolete in future versions of Nozzle.
Usage
setSignificantEntity(report, ...)
setSoftwareName 69
Arguments
report Report element.
... List of strings that will be concatenated to form the name of the entities.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
setSoftwareName Set the name of the software that used Nozzle to generate report, e.g."My Report Generator Script".
Description
Set the name of the software that used Nozzle to generate report, e.g. "My Report GeneratorScript".
Usage
setSoftwareName(report, ...)
Arguments
report Report element.
... One or more strings that will be concatenated to form the name of the software.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
70 setTableFile
setSoftwareVersion Set the name of the software that used Nozzle to generate report, e.g."Version 1.2".
Description
Set the name of the software that used Nozzle to generate report, e.g. "Version 1.2".
Usage
setSoftwareVersion(report, ...)
Arguments
report Report element.... One or more strings that will be concatenated to form the version of the software.
Value
Updated report element.
Author(s)
Nils Gehlenborg <[email protected]>
setTableFile Set path or URL of file associatd with table element.
Description
Set path or URL of file associatd with table element.
Usage
setTableFile(element, file)
Arguments
element Table element.file Path or URL to file.
Value
Updated element.
Author(s)
Nils Gehlenborg <[email protected]>
TABLE.SIGNIFICANT.DIGITS 71
TABLE.SIGNIFICANT.DIGITS
Default number of significant digits to be used to trim numericcolumns in tables.
Description
Default number of significant digits to be used to trim numeric columns in tables.
Usage
TABLE.SIGNIFICANT.DIGITS
Format
num 2
writeReport Write report to file.
Description
Write report to file.
Usage
writeReport(report, filename = DEFAULT.REPORT.FILENAME,debug = FALSE, output = c(HTML.REPORT, RDATA.REPORT),credits = TRUE, level = PROTECTION.PUBLIC,debugCss = NA, debugJavaScript = NA)
Arguments
report The report to be written.
filename Name of the output file without file extension.
debug If TRUE, external CSS (debugCss) and JavaScript (debugJavaScript) can besupplied.
output A list of output formats. Any combination of HTML.REPORT and RDATA.REPORTis allowed.
credits If TRUE, a note and a link will be included at the bottom of the report to indicatethat it was created with Nozzle.
72 writeReport
level The protection level of the report. If set to PROTECTION.PUBLIC only ele-ments with protection level PROTECTION.PUBLIC (default) will be includedin the report. If set to PROTECTION.GROUP, then all elements with protectionlevel PROTECTION.PUBLIC and PROTECTION.GROUP will be included. Ifset to PROTECTION.PRIVATE all elements will be included.
debugCss A path or URL to a CSS file that should be used instead of the built-in CSS.Only used if debug is TRUE.
debugJavaScript
A path or URL to a JavaScript file that should be used instead of the built-inJavaScript. Only used if debug is TRUE.
Author(s)
Nils Gehlenborg <[email protected]>
Index
∗Topic datasetsDEFAULT.DOI.RESOLVER, 15DEFAULT.REPORT.FILENAME, 15DEFAULT.SIGNIFICANT.ENTITY, 16HTML.FRAGMENT, 36HTML.REPORT, 37IMAGE.TYPE.PDF, 37IMAGE.TYPE.RASTER, 37IMAGE.TYPE.SVG, 38LOGO.BOTTOM.CENTER, 39LOGO.BOTTOM.LEFT, 40LOGO.BOTTOM.RIGHT, 40LOGO.TOP.CENTER, 40LOGO.TOP.LEFT, 41LOGO.TOP.RIGHT, 41PROTECTION.GROUP, 51PROTECTION.PRIVATE, 52PROTECTION.PUBLIC, 52PROTECTION.TCGA, 52RDATA.REPORT, 53SECTION.CLASS.META, 53SECTION.CLASS.RESULTS, 53TABLE.SIGNIFICANT.DIGITS, 71
∗Topic packageNozzle.R1-package, 4
addTo, 5addToInput, 6addToIntroduction, 6addToMeta, 7addToMethods, 7addToOverview, 8addToReferences, 9addToResults, 9addToSummary, 10asCode, 10asEmph, 11asFilename, 11asLink, 12asParameter, 12
asReference, 13asStrong, 13asSummary, 14asValue, 14
DEFAULT.DOI.RESOLVER, 15DEFAULT.REPORT.FILENAME, 15DEFAULT.SIGNIFICANT.ENTITY, 16
getContactInformationEmail, 16getContactInformationLabel, 17getContactInformationMessage, 17getContactInformationSubject, 18getCopyrightOwner, 18getCopyrightStatement, 19getCopyrightUrl, 19getCopyrightYear, 20getCreatorDate, 20getCreatorName, 21getCustomPrintCss, 21getCustomScreenCss, 22getDoi, 22getDoiCreator, 23getDoiPublisher, 23getDoiResolver, 24getDoiTitle, 24getDoiVersion, 25getDoiYear, 25getExportedElement, 26getExportedElementIds, 26getFigureFile, 27getFigureFileHighRes, 28getGoogleAnalyticsId, 28getLogo, 29getMaintainerAffiliation, 29getMaintainerEmail, 30getMaintainerName, 30getRendererDate, 31getRendererName, 31getReportId, 32
73
74 INDEX
getReportSubTitle, 32getReportTitle, 33getSignificantEntity, 33getSignificantResultsCount, 34getSoftwareName, 34getSoftwareVersion, 35getSummary, 35getTableFile, 36
HTML.FRAGMENT, 36HTML.REPORT, 37
IMAGE.TYPE.PDF, 37IMAGE.TYPE.RASTER, 37IMAGE.TYPE.SVG, 38isFigure, 38isTable, 39
LOGO.BOTTOM.CENTER, 39LOGO.BOTTOM.LEFT, 40LOGO.BOTTOM.RIGHT, 40LOGO.TOP.CENTER, 40LOGO.TOP.LEFT, 41LOGO.TOP.RIGHT, 41
newCitation, 41newCustomReport, 42newFigure, 43newHtml, 43newJournalCitation, 44newList, 45newParagraph, 45newParameterList, 46newReport, 47newResult, 47newSection, 48newSubSection, 49newSubSubSection, 49newTable, 50newWebCitation, 51nozzle (Nozzle.R1-package), 4Nozzle.R1-package, 4
PROTECTION.GROUP, 51PROTECTION.PRIVATE, 52PROTECTION.PUBLIC, 52PROTECTION.TCGA, 52
RDATA.REPORT, 53
SECTION.CLASS.META, 53SECTION.CLASS.RESULTS, 53setContactInformation, 54setCopyright, 54setCustomPrintCss, 55setCustomScreenCss, 56setDoi, 56setDoiCreator, 57setDoiPublisher, 58setDoiResolver, 58setDoiTitle, 59setDoiVersion, 60setDoiYear, 60setFigureFile, 61setFigureFileHighRes, 62setGoogleAnalyticsId, 62setLogo, 63setMaintainerAffiliation, 64setMaintainerEmail, 64setMaintainerName, 65setNextReport, 65setParentReport, 66setPreviousReport, 67setReportSubTitle, 67setReportTitle, 68setSignificantEntity, 68setSoftwareName, 69setSoftwareVersion, 70setTableFile, 70
TABLE.SIGNIFICANT.DIGITS, 71
writeReport, 71